19-44898511-CTT-CTTT

Position:

• chr19-44898511-CTT-CTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001128917.2(TOMM40):​c.644-2206dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.24 (1688 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: TOMM40 NM_001128917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

Genes affected

TOMM40 (HGNC:18001): (translocase of outer mitochondrial membrane 40) The protein encoded by this gene is localized in the outer membrane of the mitochondria. It is the channel-forming subunit of the translocase of the mitochondrial outer membrane (TOM) complex that is essential for import of protein precursors into mitochondria. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TOMM40	NM_001128917.2	c.644-2206dupT		intron_variant		ENST00000426677.7	NP_001122389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TOMM40	ENST00000426677.7	c.644-2206dupT		intron_variant		1	NM_001128917.2	ENSP00000410339.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 22914 AN: 97464 Hom.: 1687 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.235 AC: 22915 AN: 97450 Hom.: 1688 Cov.: 0 AF XY: 0.224 AC XY: 10023 AN XY: 44686

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.0686

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.258

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34896370; hg19: chr19-45401768;